knitr::opts_knit$set(root.dir = '../../')
Overall Activation
source('scripts/my_r.R')
library(feather)
## Warning: package 'feather' was built under R version 3.3.2
library(ggplot2)
library(reshape2)
library(bsselectR)
info <- c('Type1', 'newseq.matchgc.Noonan', 'motif_activation')
pos <- load_and_melt('pattern/Type1/newseq.matchgc.Noonan/motif_activation/pattern_positive.feather')
neg <- load_and_melt('pattern/Type1/newseq.matchgc.Noonan/motif_activation/pattern_negative.feather')
ggplot(pos$table.melted) + geom_raster(aes(x = variable, y = id, fill = value)) + scale_fill_gradient2() + ggtitle('Activation per sequence (Positive)') + labs(x = 'motif', y = 'sequence')
ggplot(neg$table.melted) + geom_raster(aes(x = variable, y = id, fill = value)) + scale_fill_gradient2() + ggtitle('Activation per sequence (Negative)') + labs(x = 'motif', y = 'sequence')
Per Motif Activation
pvalues <- c()
motifs <- c()
for(i in colnames(pos$table)){
if(i != 'id'){
poss <- pos$table[[i]]
negs <- neg$table[[i]]
pvalues <- c(pvalues, wilcox.test(poss, negs)$p.value)
motifs <- c(motifs, i)
}
}
df <- data.frame(motif=motifs, p.value=pvalues)
Motif activation comparison (positive vs negative)
